Using multiple network ports

[MrHW]

New poster here so I hope I have put this in the correct forum.

The Setup:
Hardware wise - Raspberry Pi 3 connected to an external USB hub. Connected to the external USB are three (3) LAN9512 USB to Ethernet ports. (Note: the LAN9512 is the same chip used in the original Raspberry Pi B and the same family as the LAN9514 used on the Raspberry Pi 3 thus ensuring there is a driver available in Raspbian.)

Software wise - Raspbian Jessie SD card built from NOOBS 1.8.0 and SD card built from NOOBS 1.9.2 (see The Problem below). Script to set the MAC address of each of the three external Ethernet ports run from crontab @reboot (not sure that this is the best way to handle setting the MAC addresses but it is working). All ports are DHCP and ifconfig shows that all is well, different MACs, different IPs.

The Problem:
With the NOOBS 1.8.0 everything is working fine. I can setup multiple pings from multiple of the network ports at the same time.

However, when using the NOOBS 1.9.2 version things get flaky. On boot / reboot I can ping out of one port for a bit. The "bit" may be 100 pings or 1,000s of pings. At some point the pings will fail and instead of being:
64 bytes from 8.8.8.8: icmp_seq=1250 ttl=39 time=38.4 ms
it will be:
From 192.168.10.111 icmp_seq=1305 Destination Host Unreachable.

Rarely will it ping more than one Ethernet port at the same time. Connecting a second port sometimes will cause the first port to quit pinging. And once a port has become "disconnected" i.e. "Destination Host Unreachable" none of the ports can reach the network even though ifconfig indicates that they are all alive and well.

Another clue: ifconfig shows an inet6 address on eth3 even though that port is not connected to the network nor has ever been connected to the network since a boot / reboot. It is even showing the inet6 address even when no network ports have been connected since the boot.

Thanks for any and all help. Please be a specific as possible as I am neither a Linux / Raspbian guru nor a networking guru.

[fruitoftheloom]

What happens if you install Raspbian Jessie WITHOUT using NoobS ??

[MrHW]

What happens if you install Raspbian Jessie WITHOUT using NoobS ??

fruitoftheloom thank you for your reply.

I downloaded and created an SD card with the current Raspbian Jessie image, 4.4 2016-05-27. Made no changes to the image except to add my script that sets the MAC addresses for the 3 external Ethernet ports. I ran the script manually.

I tested each Ethernet port by pinging 45.79.86.38 one port at a time. Each port would ping for a couple thousand times, different number of times on each port, and then fail with the message "Destination Host Unreachable". After a port has "failed" it will not get a good network connection without a reboot (or possibly some sort of manual intervention that I do not know of).

Additional information: When the network cable is first plugged into one of the Ethernet ports ifconfig reports that it has an IP address of 192.168.10.x which means that it has connected to my network. However, after the ping has failed ifconfig reports that the IP address is 169.254.x.x indicating that it can no longer "find" my network. From a hardware standpoint the Ethernet chips do see that it is connected to a network.